We looked at Tripline (good for plotting points on a map) and Animaps (a pretty amazing tool for making animated maps with popups). I tried to show you MapBox, which in theory lets you design complex maps in a variety of custom styles, but is also insanely complicated.
National Geographic also has a map-making application that ought to let you choose different styles, add text and markers, and pre-made data sets. It's also more print-friendly than these others. Last I checked, I couldn't get any of the features to work, though. Hopefully it's just me, or some kind of temporary glitch.